UniProt

MCP server for UniProt protein data access

python

10

GitHub Stars

python

Language

6 months ago

First Indexed

2 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "takumiy235-uniprot-mcp-server": {
      "command": "uv",
      "args": [
        "--directory",
        "path/to/uniprot-mcp-server",
        "run",
        "uniprot-mcp-server"
      ]
    }
  }
}

You can access UniProt protein information through a dedicated MCP server that serves as a lightweight bridge between AI assistants and the UniProt data. It supports single and batch queries, caches results to speed responses, and provides structured protein details such as name, function, sequence, length, and organism.

How to use

You interact with the server through an MCP client. To get protein data, request information for a single UniProt accession by providing its accession number, or ask for multiple accessions to compare results. The server handles common issues like slow responses or invalid accession numbers and returns detailed protein records including name, function description, full sequence, sequence length, and organism.

How to install

Prerequisites: Python 3.10 or higher is required.

Clone the project repository.
Change into the project directory.
Install dependencies using the recommended runner.

uv pip install -r requirements.txt

# Or, if you prefer to use plain pip
pip install -r requirements.txt

Configuration

Configure the MCP server to run locally. The following configuration starts the server using the local directory that contains the MCP code and runs the uniprot-mcp-server entry.

{
  "mcpServers": {
    "uniprot": {
      "command": "uv",
      "args": ["--directory", "path/to/uniprot-mcp-server", "run", "uniprot-mcp-server"]
    }
  }
}

Available tools

get_protein_info

Fetch information for a single UniProt accession, returning protein name, function, sequence, length, and organism.

get_batch_protein_info

Fetch information for multiple UniProt accessions in a single operation, returning a list of protein information objects.